Related papers: A processing and analytics system for microscopy d…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
We present an end-to-end automated workflow that uses large-scale remote compute resources and an embedded GPU platform at the edge to enable AI/ML-accelerated real-time analysis of data collected for x-ray ptychography. Ptychography is a…
We present pyroomacoustics, a software package aimed at the rapid development and testing of audio array processing algorithms. The content of the package can be divided into three main components: an intuitive Python object-oriented…
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To…
Microarray technology is still an important way to assess gene expression in molecular biology, mainly because it measures expression profiles for thousands of genes simultaneously, what makes this technology a good option for some studies…
Software supply chain attacks have revealed blind spots in existing SCA tools, which are often limited to a single ecosystem and assess either software artifacts or community activity in isolation. This fragmentation across tools and…
The Dynamic PicoProbe at Argonne National Laboratory is undergoing upgrades that will enable it to produce up to 100s of GB of data per day. While this data is highly important for both fundamental science and industrial applications, there…
We propose a framework to develop cyber solutions to support the remote steering of science instruments and measurements collection over instrument-computing ecosystems. It is based on provisioning separate data and control connections at…
To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent -- a popular feature-rich framework for sequence-based…
We introduce pymovements: a Python package for analyzing eye-tracking data that follows best practices in software development, including rigorous testing and adherence to coding standards. The package provides functionality for key…
A large amount of data is produced every second from modern information systems such as mobile devices, the world wide web, Internet of Things, social media, etc. Analysis and mining of this massive data requires a lot of advanced tools and…
PySDM is an open-source Python package for simulating the dynamics of particles undergoing condensational and collisional growth, interacting with a fluid flow and subject to chemical composition changes. It is intended to serve as a…
Behavioral studies using personal digital devices typically produce rich longitudinal datasets of mixed data types. These data provide information about the behavior of users of these devices in real-time and in the users' natural…
Bright-field microscopy, a cost-effective solution for live-cell culture, is often the only resource available, along with standard CPUs, for many low-budget labs. The inherent challenges of bright-field images -- their noisiness, low…
Recent advances in (scanning) transmission electron microscopy have enabled routine generation of large volumes of high-veracity structural data on 2D and 3D materials, naturally offering the challenge of using these as starting inputs for…
This article presents a high-throughput computer program, called EasyDD, for batch processing, analyzing and visualizing of spectral data; particularly those related to the new generation of synchrotron detectors and X-ray powder…
The introduction of large language models and other influential developments in AI-based language processing have led to an evolution in the methods available to quantitatively analyse language data. With the resultant growth of attention…
We present PyWiFeS, a new Python-based data reduction pipeline for the Wide Field Spectrograph (WiFeS). PyWiFeS consists of a series of core data processing routines built on standard scientific Python packages commonly used in astronomical…
Selecting third-party software packages in open-source ecosystems like Python is challenging due to the large number of alternatives and limited transparent evidence for comparison. Generative AI tools are increasingly used in development…